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helena-bioinformatics

Noodle Biomedical Literature Discovery MCP

Official

Explore a PMID literature neighborhood

get_publication_neighborhood
Read-onlyIdempotent

Retrieve the citation and semantic neighborhood around a single PubMed ID to uncover related biomedical publications for literature discovery and professional review.

Instructions

Retrieve the bounded citation and semantic neighborhood around one PMID. Results are for literature discovery and professional review, not diagnosis or treatment.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
pmidYesOne PubMed identifier, as 1 to 12 digits.
from_work_idNoOptional prior work ID for a reversible graph path.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
edgesYes
nodesYes
freshnessYes
anchor_pmidNo
stale_afterYes
generated_atYes
graph_versionYes
anchor_node_idYes
anchor_work_idNo
policy_versionYes
usage_boundaryYes
release_channelYes
contract_versionYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv0.2.1

TDQS

B3.4/5.0
Behavior3/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations already declare readOnlyHint, idempotentHint, and destructiveHint, covering the safety profile. The description adds useful context like 'bounded neighborhood' and a disclaimer about non-clinical use, which go beyond metadata. However, it does not explain specific behaviors such as pagination or limits, so it provides only moderate added value.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is two concise sentences with no filler. The core action is front-loaded, and the disclaimer is brief. Every word contributes to clarity, making it an exemplar of efficient writing.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

For a read-only tool with an output schema and annotations covering safety, the description provides sufficient context. It states the purpose and the non-clinical usage, which is important. The only gap is the lack of explicit differentiation from get_work_neighborhood, but that falls under usage guidance rather than completeness. Overall, it is well-rounded for the tool's complexity.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 100%, with both pmid and from_work_id fully documented in the schema. The description adds no additional parameter-specific details, so it does not exceed the baseline score for a high-coverage schema. The agent can rely on the schema for parameter meaning.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description uses a specific verb ('Retrieve') and resource ('bounded citation and semantic neighborhood') scoped to one PMID. It clearly identifies the tool's function, but does not explicitly distinguish it from sibling get_work_neighborhood, which is a closely related alternative. The name and title help, but explicit differentiation is absent.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines2/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

No guidance is provided on when to use this tool versus alternatives. There is no mention of conditions like 'use for PMID-based exploration' or reference to sibling tools. The description simply states what it does, leaving the agent to infer appropriate usage from context.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.